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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<title>Academia and Open Source: PyCon 2017</title>
<link rel="stylesheet" href="css/reveal.css">
<link rel="stylesheet" href="css/theme/simple.css">
<!-- Theme used for syntax highlighting of code -->
<link rel="stylesheet" href="lib/css/zenburn.css">
<!-- Printing and PDF exports -->
<script>
var link = document.createElement( 'link' );
link.rel = 'stylesheet';
link.type = 'text/css';
link.href = window.location.search.match( /print-pdf/gi ) ? 'css/print/pdf.css' : 'css/print/paper.css';
document.getElementsByTagName( 'head' )[0].appendChild( link );
</script>
</head>
<body>
<div class="reveal">
<div class="slides">
<section>
<h2>Academia and Open Source</h2>
<h3>SciPy 2017</h3>
<h4>Austin, TX</h4>
<h4>July 12, 2017</h4>
<br/>
<h3>Kathryn (Katy) Huff</h3>
</section>
<section>
<section data-background-image="./images/olive_trees_on_thassos_cropped.JPG" data-background-size="cover">
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/9/94/Sanzio_01.jpg" data-background-size="cover">
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/9/94/Sanzio_01.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
<blockquote
cite="https://www.uillinois.edu/about/mission/">
“... transform lives and serve society by educating, creating knowledge, and putting knowledge to work on a large scale and with excellence.
”
- University of Illinois Mission Statement, 2017
</blockquote>
</section>
<section data-background-image="./images/lecture-hall.jpg" data-background-size="cover">
</section>
<section>
<span class="fragment">
<a
href="http://tams.unt.edu"
class="image"><img
height="200"
src="./images/tams.jpg"
alt="Texas Academy of Mathematics and Science"></a>
</span>
<span class="fragment">
<a
href="http://uchicago.edu"
class="image"><img
height="200"
src="http://geosci.uchicago.edu/~kite/university.seal.rgb.maroon.jpg"
alt="Physics, University of Chicago"></a>
</span>
<span class="fragment">
<a
href="https://engr.wisc.edu/ep.html"
class="image"><img
height="200"
src="https://biochem.wisc.edu/sites/default/files/intranet/medialab/clipart/UW_crest.gif"
alt="Nuclear Engineering and Engineering Physics, University of Wisconsin - Madison"></a>
</span>
<span class="fragment">
<a
href="http://nuc.berkeley.edu"
class="image"><img
height="200"
src="http://www.berkeley.edu/brand/img/seals/ucbseal_139_540.png"
alt="Nuclear Engineering, University of California, Berkeley"></a>
</span>
<span class="fragment"> <a href="http://thehackerwithin.github.io/illinois" class="image"><img height="200" src="https://upload.wikimedia.org/wikipedia/en/thumb/1/18/UIUC_seal.svg/600px-UIUC_seal.svg.png" alt="UIUC THW"></a> </span>
</section>
<section>
<span class="fragment">
<a
href="http://scipy.org"
class="image"><img
height="100"
src="http://scipy.org/_static/images/scipycentral.png"
alt="Scipy"></a>
</span>
<span class="fragment">
<a
href="http://thehackerwithin.github.io"
class="image"><img
height="100"
src="http://thehackerwithin.github.io/images/thw_icon.png"
alt="THW"></a>
</span>
<span class="fragment">
<a
href="http://software-carpentry.org"
class="image"><img
height="100"
src="http://bids.berkeley.edu/sites/default/files/styles/450x254/public/projects/software-carpentry-450x254.png?itok=0XnUCwrr"
alt="Software Carpentry"></a>
</span>
<span class="fragment">
<a
href="http://datacarpentry.org"
class="image"><img
height="100"
src="./images/data-carpentry.png"
alt="Data Carpentry"></a>
</span>
<span class="fragment">
<a
href="http://joss.theoj.org"
class="image"><img
height="100"
src="./images/joss.png"
alt="JOSS"></a>
</span>
<br/>
<span class="fragment">
<a href="http://bids.berkeley.edu"
class="image"><img
height="100"
src="http://bids.berkeley.edu/sites/all/themes/bids/logo.png"
alt="BIDS Logo"></a>
</span>
<span class="fragment">
<a
href="http://physics.codes"
class="image"><img
height="200"
src="http://physics.codes/images/ecip.jpg"
alt="book"></a>
</span>
<span class="fragment">
<a
href="http://http://www.ucpress.edu/book.php?isbn=9780520294752"
class="image"><img
height="200"
src="./images/2016-prr-book.jpg"
alt="book"></a>
</span>
<!-- <br/>
<span class="fragment">
<a
href="http://ncsa.illinois.edu"
class="image"><img
height="100"
src="http://www.ncsa.illinois.edu/assets/img/logos_ncsa.png"
alt="NCSA Logo"></a>
</span>
<span class="fragment">
<a
href="http://arfc.npre.illinois.edu"
class="image"><img
height="150"
src="./images/arfc-logo.png"
alt="ARFC Logo"></a>
</span>
-->
</section>
<section>
<a href="http://rationalwiki.org/w/images/thumb/0/0e/Fission.svg/800px-Fission.svg.png"
class="image"><img
height="100%"
src="http://rationalwiki.org/w/images/thumb/0/0e/Fission.svg/800px-Fission.svg.png"
alt="Fission."></a>
</section>
<section>
<a href="http://rationalwiki.org/w/images/thumb/1/1f/Chainreaction.svg/715px-Chainreaction.svg.png"
class="image"><img
height="500"
src="http://rationalwiki.org/w/images/thumb/1/1f/Chainreaction.svg/715px-Chainreaction.svg.png"
alt="Chain reaction"></a>
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/a/a0/PressurizedWaterReactor.gif" data-background-size="contain">
</section>
<section data-background-image="./images/jvn-rf-su.jpg" data-background-size="cover">
</section>
<section data-background-image="./images/jvn-rf-su.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
<blockquote cite="john von neumann">
“I am thinking about something
much more important than bombs. I am
thinking about computers.” - John
von Neumann, 1946.
</blockquote>
</section>
</section>
<section>
<section>
<h2>Education</h2>
<h3>must...</h3>
<ul>
<li class="fragment">transfer knowledge,</li>
<li class="fragment">communicate concepts,</li>
<li class="fragment">convey how to think,</li>
<li class="fragment">prepare learners for their futures.</li>
</ul>
<p class="fragment"><b>But computers have changed everything.</b></p>
</section>
<section>
<h2>The Hacker Within is Helping</h2>
</section>
<section data-background="./images/thwlogo_dark_bg.png" data-background-size="cover">
</section>
<section data-background="./images/thwlogo_dark_bg.png" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<p class="fragment">Peer-led organization for scientific computing best practices.</p>
</section>
<section>
<a
href="http://katyhuff.github.io/2015-11-06-ncsa/images/2015-01-28.jpg"
class="image"><img
src="./images/2015-01-28.jpg"
alt="THW at BIDS"></a>
</section>
<section>
<span class="fragment">
<a
href="https://engr.wisc.edu/ep.html"
class="image"><img
height="200"
src="https://biochem.wisc.edu/sites/default/files/intranet/medialab/clipart/UW_crest.gif"
alt="Nuclear Engineering and Engineering Physics, University of Wisconsin - Madison"></a>
</span>
<span class="fragment">
<a
href="http://nuc.berkeley.edu"
class="image"><img
height="200"
src="http://www.berkeley.edu/brand/img/seals/ucbseal_139_540.png"
alt="Nuclear Engineering, University of California, Berkeley"></a>
</span>
<span class="fragment">
<span class="fragment fade-out">
<a href="http://melbourne.resbaz.edu.au/"
class="image"><img
height="200"
src="http://ceasar.acems.org.au/images/UOM-Pos3D_S_sm.png"
alt="melbourne"></a>
</span>
</span>
<span class="fragment">
<span class="fragment fade-out">
<a
href="http://msu.edu"
class="image"><img
height="200"
src="https://www.msu.edu/~rollerbe/MSU%20Seal%20Green.jpg"
alt="Michigan State"></a>
</span>
</span>
<span class="fragment">
<span class="fragment fade-out">
<a href="http://thehackerwithin.github.io/yale"
class="image"><img
height="200"
src="https://upload.wikimedia.org/wikipedia/commons/2/24/Yale_University_Logo.jpg"
alt="Yale"></a>
</span>
</span>
<span class="fragment">
<a href="http://thehackerwithin.github.io/swinburne"
class="image"><img
height="200"
src="http://static1.squarespace.com/static/52541308e4b05048ea3ab82a/t/53ec22ede4b0227480ca8509/1407895562993/Swinburne+University+of+Technology+.jpg?format=1000w"
alt="swinburne"></a>
</span>
<span class="fragment">
<span class="fragment fade-out">
<a href="http://thehackerwithin.github.io/davis"
class="image"><img
height="200"
src="./images/uc-davis-seal.png"
alt="Davis THW"></a>
</span>
</span>
<span class="fragment">
<a href="http://thehackerwithin.github.io/illinois"
class="image"><img
height="200"
src="https://upload.wikimedia.org/wikipedia/en/thumb/1/18/UIUC_seal.svg/600px-UIUC_seal.svg.png"
alt="UIUC THW"></a>
</span>
</section>
<section>
<h1>Community</h1>
<ul>
<li>democratic anarchy</li>
<li>maximize permissions</li>
<li>charismatic leadership</li>
<li>occasional beer</li>
</ul>
</section>
<section>
<a href="thehackerwithin.github.io"
class="image"><img
src="./images/2010-01-14.jpg"
alt="excellent team"></a>
</section>
<section>
<h1>Peer-Driven</h1>
<ul>
<li>peer teaching and learning</li>
<li>interdisciplinary normalizes mixed skill levels</li>
<li>relevant topics</li>
<li>appeals to the desire to show off</li>
<li>direct peer-to-peer skill sharing</li>
</ul>
</section>
<section>
<iframe src="http://thehackerwithin.github.io/berkeley/previous.html" width="100%" height=600 frameborder="0" marginwidth="0" marginheight="0" scrolling="yes" style="border:0px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe>
</section>
<section>
<a
href="http://thehackerwithin.github.io/images/cpp_boot1.jpg"
class="image"><img
height="700"
src="http://thehackerwithin.github.io/images/cpp_boot1.jpg"
alt="SC Bootcamp 2"></a>
</section>
<section>
<a href="http://thehackerwithin.github.io/images/sc_boot.jpg"
class="image"><img
height="700"
src="http://thehackerwithin.github.io/images/sc_boot.jpg"
alt="SC Bootcamp 1"></a>
</section>
<section>
<a href="http://thehackerwithin.github.io/images/pybc.jpg"
class="image"><img
height="700"
src="http://thehackerwithin.github.io/images/pybc.jpg"
alt="Python Bootcamp "></a>
</section>
<section>
<a
href="http://thehackerwithin.github.io/images/hunter.jpg"
class="image"><img
height="700"
src="http://thehackerwithin.github.io/images/hunter.jpg"
alt="hunter"></a>
</section>
<section>
<a href="http://thehackerwithin.github.io/images/scbc.jpg"
class="image"><img
height="700"
src="http://thehackerwithin.github.io/images/scbc.jpg"
alt="scbc"></a>
</section>
</section>
<section>
<section>
<h2>The Carpentries are Helping</h2>
</section>
<section>
<span class="fragment">
<a href="https://twitter.com/hackerwithin/status/606564957698715650"
class="image"><img
height="900"
src="https://pbs.twimg.com/media/CGrzm_aUQAAUt-n.jpg"
alt="workshop"></a>
</span>
</section>
<section>
<h2>Software Carpentry Workshops</h2>
<ul>
<li>Two days of hands-on learning</li>
<li>Scientists teaching scientists</li>
<li>Instructors are volunteers</li>
<li>Materials are all open access</li>
</ul>
</section>
<section>
<iframe
src="http://software-carpentry.org/workshops/previous.html"
width="1200" height="500"
style="-webkit-transform:scale(1.1);-moz-transform-scale(1.1);"></iframe>
</section>
<section>
<span class="fragment">
<a href="http://nbviewer.ipython.org/github/katyhuff/2015-11-06-ncsa/blob/master/swc/swc_plots.ipynb#"
class="image"><img
height="600"
src="./images/workshops.png"
alt="workshops"></a>
</span>
</section>
<section>
<iframe
src="http://software-carpentry.org/pages/team.html"
width="1200" height="500"
style="-webkit-transform:scale(1.1);-moz-transform-scale(1.1);"></iframe>
</section>
<section data-background="./images/all.png" data-background-size="cover">
</section>
</section>
<section>
<section>
<h2>The Only Sustainable Solution</h2>
<h3>Will Infuse Traditional Curriculum with Computing</h3>
</section>
<section>
<h2>How?</h2>
<ul>
<li><b>open source</b> <span class="fragment"> for collaboration</span></li>
<li><b>example-driven</b> <span class="fragment"> for <a href="https://computinged.wordpress.com/tag/contextualized-computing-education/">contextual computation</a></span></li>
<li><b>project-focused </b><span class='fragment'> with incremental assignments</span> </li>
<li><b>using proven pedagogy </b><span class="fragment"> backed by science</li>
<li><b>and using modern tools </b><span class="fragment"> like nbgrader</li>
</ul>
</section>
<section>
<h2>NBGrader: Jess Hamrick</h2>
<img
src="https://github.com/jupyter/nbgrader/blob/master/nbgrader/docs/source/user_guide/images/creating_assignment.gif?raw=true"
height="600">
</section>
<section>
<h3>Data Science 8</h3>
<p>Cathryn Carson, David Culler, etc. <a href="data.berkeley.edu">data.berkeley.edu</a></p>
<blockquote class="twitter-tweet tw-align-center" data-lang="en"><p lang="en" dir="ltr">A cloud based workflow for data science education at UC Berkeley <a href="https://twitter.com/NSF_CISE">@NSF_CISE</a> <a href="https://twitter.com/hashtag/DataScience?src=hash">#DataScience</a> <a href="https://t.co/evzJ4orBf7">pic.twitter.com/evzJ4orBf7</a></p>— Eddie Fuller (@ef_math) <a href="https://twitter.com/ef_math/status/875013213112459264">June 14, 2017</a></blockquote>
<script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script>
</section>
<section>
<h2>Teaching with Notebooks: Lorena Barba</h2>
<iframe
src="http://nbviewer.ipython.org/github/barbagroup/CFDPython/blob/master/lessons/01_Step_1.ipynb"
width="100%" height=800
scrolling="yes">. </iframe>
</section>
<section>
<h3>Teaching with Notebooks: Lots of Others</h3>
<iframe
src="http://nbviewer.jupyter.org/github/katyhuff/npre412/blob/master/in-core/in-core.ipynb"
width="100%" height=600
scrolling="yes"
allowfullscreen>. </iframe>
</section>
<section>
<h3>PrairieLearn Course Management</h3>
<h3>(Prof. Matt West et al.)</h3>
<iframe
src="http://prairielearn.readthedocs.io/en/latest/"
width="100%" height=600
scrolling="yes"
allowfullscreen>. </iframe>
</section>
<section>
<h3>RELATE Course Management</h3>
<h3>(Prof. Andreas Kloeckner et al.)</h3>
<img src="https://documen.tician.de/relate/_images/screenshot.png">
<img src="https://documen.tician.de/relate/_images/screenshot-2.png">
</section>
</section>
<section>
<section data-background-image="./images/jvn-rf-su.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
<blockquote cite="Donoho, Reproducible
Research in
Computational Harmonic Analysis,
2009.">
“
The scientific method’s central
motivation is the ubiquity of error—the
awareness
that mistakes and self-delusion can
creep in
absolutely anywhere and that the
scientist’s effort
is primarily expended in recognizing
and rooting
out error.
” - Donoho, 2009.
</blockquote>
</section>
<section>
<span class="fragment">
<a
href="http://http://www.ucpress.edu/book.php?isbn=9780520294752"
class="image"><img
height="700"
src="./images/2016-prr-book.jpg"
alt="book"></a>
</span>
</section>
<section data-background="./images/book_stock_pexels.jpg" data-background-size="cover">
</section>
<section data-background="./images/book_stock_pexels.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<p class="fragment">''Reading
brings us
unknown
friends''
- Honore de
Balzac</p>
</section>
<section data-background="./images/book_stock_pexels.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<p>
<ul>
<li>BIDS</li>
<li>Justin Kitzes</li>
<li>Fatma Imamoglu</li>
<li>Daniel Turek</li>
<li>Ben Marwick</li>
<li>Chapter Authors</li>
<li>Case Study Authors</li>
<li>Reproducibility Working Group</li>
</ul>
<br/>
<span class="fragment">
<a href="http://bids.berkeley.edu"
class="image"><img
width="25%"
src="http://bids.berkeley.edu/sites/all/themes/bids/logo.png"
alt="BIDS Logo"></a>
</span>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<a href="http://bids.berkeley.edu"
class="image"><img
height="500"
src="images/repro_wg_mission.png"
alt="repro mission"></a>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<a href="http://bids.berkeley.edu"
class="image"><img
height="500"
src="images/jkitzes_flow_raw.png"
alt="justin kitzes flow"></a>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<a href="http://bids.berkeley.edu"
class="image"><img
height="500"
src="images/jkitzes_flow.png"
alt="justin kitzes flow"></a>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<span class="fragment">
<a href="http://bids.berkeley.edu"
class="image"><img
height="500"
src="images/khuff_flow.png"
alt="khuff flow"></a>
</span>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<span class="fragment">
<a href="http://bids.berkeley.edu"
class="image"><img
height="300"
src="images/basic_flow.png"
alt="basic flow"></a>
</span>
</section>
<section data-background="./images/repro_conf.jpg" data-background-size="cover">
</section>
<section data-background="./images/repro_conf.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<a
href="https://github.com/BIDS/repro-conf"
data-preview-link><h3>Reproducibility
and Open
Science
Conference</h3>
<h4>May 21&22, 2015</h4></a>
<ul>
<li>Three days</li>
<li>Invitation Only</li>
<li>Case Studies, Education, Self-assessment</li>
<li>https://github.com/BIDS/repro-conf</li>
</ul>
</section>
<section data-background="./images/repro_conf.jpg" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<span class="fragment">
<a href="http://bids.berkeley.edu"
class="image"><img
height="500"
src="images/jgukelberger_flow.png"
alt="jgukelberger flow"></a>
</span>
</section>
<section data-background="./images/repro_conf.jpg" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<span class="fragment">
<a href="http://bids.berkeley.edu"
class="image"><img
height="500"
src="images/akrause_flow.png"
alt="akrause flow"></a>
</span>
</section>
<section data-background="./images/repro_conf.jpg" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<ul>
<li>Incentives</li>
<li>Pain Points</li>
<li>Recommmendations from the Authors</li>
<li>A Little Data</li>
<li>Needs</li>
</ul>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<h2>Incentives</h2>
<ul>
<li>verifiability</li>
<li>collaboration</li>
<li>efficiency</li>
<li>extensibility</li>
<li>"focus on science"</li>
<li>"forced planning"</li>
<li>"safety for evolution"</li>
</ul>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<h2>Pain Points</h2>
<ul>
<li class="fragment">People and Skills</li>
<li class="fragment">Dependencies, Build Systems, and Packaging</li>
<li class="fragment">Hardware Access</li>
<li class="fragment">Testing</li>
<li class="fragment">Publishing</li>
<li class="fragment">Data Versioning</li>
<li class="fragment">Time and Incentives</li>
<li class="fragment">Data restrictions</li>
</ul>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<h3>Recommendations</h3>
<ul>
<li>version control your code</li>
<li>open your data</li>
<li>automate everywhere possible</li>
<li>document your processes</li>
<li>test everything</li>
<li>use free and open tools</li>
</ul>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<h3>Recommendations: Continued</h3>
<ul>
<li class="fragment">avoid excessive dependencies</li>
<li class="fragment">or at least package their installation</li>
<li class="fragment">host code on a collaborative platform (e.g. GitHub)</li>
<li class="fragment">get DOIs for data and code</li>
<li class="fragment">plain text data is preferred, timeless</li>
<li class="fragment">explicitly set seeds</li>
<li class="fragment">workflow frameworks can be overkill</li>
</ul>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<h3>Recommendations: Outliers</h3>
<blockquote>
... in our estimation, if someone
was to try to reproduce our research it would probably be more
natural for them to write their own scripts as this has the
additional benefit that they might not fall into any error
we may have accidentally introduced in our scripts.
</blockquote>
</section>
<section data-background="https://bids.berkeley.edu/sites/default/files/bids_dots_and_lines_overlay.png" data-background-size="cover">
</section>
<section data-background="https://bids.berkeley.edu/sites/default/files/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
<h2>Recommendations:
Outliers</h2>
<blockquote>Scientific funding and the number of scientists available to do the work is finite. Therefore not every scientific result can, or should be reproduced.</blockquote>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<a href="http://bids.berkeley.edu"
class="image"><img
height="400"
src="./images/tools.png"
alt="tools">
</a>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<a href="http://bids.berkeley.edu"
class="image"><img
height="400"
src="./images/languages.png"
alt="languagess">
</a>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<a href="http://bids.berkeley.edu"
class="image"><img
height="400"
src="./images/testing.png"
alt="testing"></a>
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover">
</section>
<section data-background="./images/bids_dots_and_lines_overlay.png" data-transition="none" data-background-size="cover" style="background: rgba(255, 255, 255, 0.95);">
<h2>Emergent Needs</h2>
<small>
<ul>
<li>Common demoninator tools should support reproducibility</li>
<li>Improved configuration and build systems</li>
<li>Reproducibility at scale for HPC</li>
<li>Standardized hardware configurations limited-availability experimental apparatuses.</li>
<li><b>Better understanding of incentives for unit testing.</b></li>
<li>Greater adoption of unit testing irrespective of programming language.</li>
<li><b>Broader community adoption around publication formats that allow parallel editing</b> </li>
<li><b>Broader adoption of data storage, versioning, and management tools.</b></li>
<li>Increased community recognition of the benefits of reproducibility.</li>
<li>Incentive systems where reproducibility is not self-incentivizing.</li>
<li>Standards around scrubbed and representational data</li>
<li><b>Community adoption for file format standards within some domains.</b></li>
<li>Domain standards which translate well outside of their own scientific communities.</li>
</ul>
</small>
</section>
</section>
<section>
<section data-background-image="./images/jvn-rf-su.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
<blockquote cite="Feynman, R. 1974 commencement address at Caltech.">
“the first principle is that you must not fool yourself, and you are the easiest person to fool.” - R. Feynman, 1974
</blockquote>
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/3/35/Dagstuhl_DSC02285.jpg" data-background-size="cover" >
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/3/35/Dagstuhl_DSC02285.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
<h3>Engineering Academic Software</h3>
<h4 class="fragment">Manifesto from Dagstuhl Perspectives Workshop
16252</h4>
<p class="fragment"><a
href="http://drops.dagstuhl.de/opus/volltexte/2017/7146/">drops.dagstuhl.de/opus/volltexte/2017/7146</a></p>
</section>
<section data-background-image="http://www.dagstuhl.de/Gruppenbilder/16252.2.B.JPG" data-background-size="contain">
</section>
<section data-background-image="http://www.dagstuhl.de/Gruppenbilder/16252.2.B.JPG" data-background-size="contain" style="background: rgba(255, 255, 255, 0.80);">
<p class="fragment">Alice Allen, Cecilia Aragon, Christoph Becker,
Jeffrey Carver, Andrei Chis, Benoit Combemale, Mike Croucher, Kevin
Crowston, Daniel Garijo, Ashish Gehani, Carole Goble, Robert Haines,
Robert Hirschfeld, James Howison, Kathryn Huff, Caroline Jay, Daniel S.
Katz, Claude Kirchner, Katie Kuksenok, Ralf Lämmel, Oscar Nierstrasz,
Matt Turk, Rob van Nieuwpoort, Matthew Vaughn, and Jurgen J. Vinju</p>
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/3/35/Dagstuhl_DSC02285.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
<blockquote
cite="http://drops.dagstuhl.de/opus/volltexte/2017/7146/">
“ Software is often a
critical component of
scientific research. It can be
a component of the academic
research methods used to
produce research results, or it
may itself be an academic
research result. Software,
however, has rarely been
considered to be a citable
artifact in its own right.
”<br>
- <a href="http://drops.dagstuhl.de/opus/volltexte/2017/7146/">
Dagstuhl Perspectives
Manifesto on Engineering
Academic Software</a>
</blockquote>
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/3/35/Dagstuhl_DSC02285.jpg" data-background-size="cover">
<a href="https://twitter.com/wesmckinn/status/741744599731830784" class="image">
<img width="100%" src="./images/wes.png" alt="Wes"></a>
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/3/35/Dagstuhl_DSC02285.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
<h2>Citation</h2>
<ul>
<li class="fragment">I will make explicit how to cite my software.</li>
<li class="fragment">I will cite the software I used to produce my research results.</li>
<li class="fragment">When reviewing, I will encourage others to cite the software they have used.</li>
</ul>
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/3/35/Dagstuhl_DSC02285.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
'I can’t figure out how to create Sage in academia. The money isn’t there. The mathematical community doesn’t care enough. The only option left is for me to build a company.'
- William Stein, 2016
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/3/35/Dagstuhl_DSC02285.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
<h2>Careers</h2>
<ul>
<li class="fragment">I will recognize software contributions in hiring and promotion within my institution, and
encourage others in my institution to do the same.</li>
</ul>
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/3/35/Dagstuhl_DSC02285.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
<a href="https://twitter.com/tweetotaler/status/884412302098915329" class="image">
<img width="100%" src="./images/tweetotaler.png" alt="Elizabeth"></a>
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/3/35/Dagstuhl_DSC02285.jpg" data-background-size="cover">
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/3/35/Dagstuhl_DSC02285.jpg" data-background-size="cover" style="background: rgba(255, 255, 255, 0.80);">
<h3>Development and Use</h3>
<font size="6">
<ul>
<li class="fragment">I will develop software as open source from the start, whenever possible.</li>
<li class="fragment">I will contribute to sustaining software I use and rely on.</li>
<li class="fragment">I will match proposed software engineering practices to the actual needs and resources of the project.</li>
<li class="fragment">I will help researchers improve the quality of their software without passing judgment.</li>
<li class="fragment">I will publish the intellectual contributions of my research software.</li>
<li class="fragment">I will document (including usage instructions, and input
and output examples), package, release, and archive versions of my
software.</li>
</ul>
</font>
</section>
</section>
<section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/Knowledge-sharing.jpg/1024px-Knowledge-sharing.jpg">
</section>
<section
data-background-image="https://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/Knowledge-sharing.jpg/1024px-Knowledge-sharing.jpg" style="background: rgba(255, 255, 255, 0.80);">
<img src="./images/joss.png">
</section>
<section data-background-image="https://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/Knowledge-sharing.jpg/1024px-Knowledge-sharing.jpg"
style="background: rgba(255, 255, 255, 0.80);">
<img src="./images/editor-montage.png" height=600>
</section>
<section
data-background-image="https://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/Knowledge-sharing.jpg/1024px-Knowledge-sharing.jpg">
<img src="./images/joss-site.png">
</section>
<section>
<iframe src=" https://arxiv.org/abs/1707.02264"
frameBorder="0" width="100%"
height="600" marginwidth="0"
marginheight="0" scrolling="yes" style="border:0px; margin-bottom:5px; max-width: 100%;"
allowfullscreen> </iframe>
</section>
</section>
<section>
<section>
<a class="twitter-timeline" href="https://twitter.com/hashtag/oschallenges" data-widget-id="884989854337175554">#oschallenges Tweets</a>
<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
</section>
<section>
<h4>SciPy Has an Intersectionality Challenge</h4>
<a class="image" href="https://www.lucidchart.com/publicSegments/view/53bc460d-3230-447c-8e68-04870a0092e1/image.png"> <img width="600" src="https://www.lucidchart.com/publicSegments/view/53bc460d-3230-447c-8e68-04870a0092e1/image.png" alt="Venn">
</a>
</section>
<section>
<h2>What's Intersectionality?</h2>
<a class="image" href="http://cornify.com">
<img width="280" height="326" src="https://s3.amazonaws.com/hakim-static/reveal-js/cornify.gif" alt="Unicorn">
</a>
</section>
<section>
<h2>No Really. What is it?</h2>
<p>
"... the study
of intersections between forms
or systems of oppression,
domination or discrimination.
An example is ... that the
experience of being a [rainbow]
[unicorn] cannot be understood in
terms of being [rainbow], and of
being [a unicorn], considered
independently, but must include
the interactions, which
frequently reinforce each
other." -- Wikipedia
</p>
</section>
<section>
<h2>Why So Few?</h2>
<p>
Scientific python seems to reside in a
technological space where the combined
diversity issues of both science and
computing <strong>compound</strong> one other to
ill-effect.
</p>
</section>
<section>
<h2>Suggestion: Cast a Wide Net</h2>
<p>
The old developers aren't diverse. So,
we need new developers to join in.
</p>
</section>
<section>
<h3>Lower the Barrier, Not Standards</h3>
<small>
<blockquote cite="http://www.amazon.com/Whistling-Vivaldi-Stereotypes-Affect-Issues/dp/0393339726">
“The feedback giver explained that he 'used high standards' in evaluating the essays for publication in the teaching magazine. Still, he said, having read the student’s essay, he believed the student could meet those standards. His criticism, this form of feedback implies, was offered to help the student meet the publication’s high standards. Black students trusted this feedback as much as white students, and trusting it powerfully motivated them to improve their essay.”
</blockquote>
</small>
<p>
<strong>-- Claude Steele, Whistling Vivaldi</strong>
</p>
</section>
<section>
<h2>Easy Suggestions</h2>
<ul>
<li class="fragment"><code> New Developer Instructions</code></li>
<li class="fragment"><code> Comprehensive Documentation</code></li>
<li class="fragment"><code> Accessible Listhost </code></li>
<li class="fragment"><code> Define Expectations Clearly </code></li>
<li class="fragment"><code> Curate Low Hanging Fruit </code></li>
<li class="fragment"><code> Give Permissions Generously </code></li>
<li class="fragment"><code> Strict Issue Assignment Workflow </code></li>
</ul>
</section>
<section>
<h2>Harder Suggestions</h2>
<ul>
<li class="fragment"><code> Targeted Sprints</code></li>
<li class="fragment"><code> Appoint an Ambassador</code></li>
<li class="fragment"><code> Mentor Users Directly</code></li>
<li class="fragment"><code> Consider Users Conferences</code></li>
</ul>
</section>
<section data-background-image="./images/pphw-kdh.jpg" data-background-size="contain">
</section>
<section data-background-image="./images/pphw-kdh.jpg" data-background-size="contain" style="background: rgba(255, 255, 255, 0.80);">
<h3>Apprenticeship</h3>
</section>
<section data-background-image="./images/pphw-kdh.jpg" data-background-size="contain" style="background: rgba(255, 255, 255, 0.80);">
<h3>Apprenticeship</h3>
<ul>
<li>Active: engagement, decision making, action, safe environment.</li>
<li>Social: interaction with tools, teachers, and beneficiaries.</li>
<li>Authentic: deeper connection to the importance of the work.</li>
</ul>
</section>
<section>
<p><a href="http://bit.ly/2tLIRPj">http://bit.ly/2tLIRPj</a></p>
<span>
<a
href="http://bids.berkeley.edu"
class="image"><img
height="300"
src="./images/nelle.png"
alt="Nelle Varoquax"></a>
</span>
<span>
<a
href="http://bids.berkeley.edu"
class="image"><img
height="300"
src="./images/chris.png"
alt="Chris Holdgraf"></a>
</span>
<span>
<a
href="http://bids.berkeley.edu"
class="image"><img